Should the Republicans succeed in scrapping the Affordable Care Act, the country’s health care system will suffer a big setback.

No, I’m not referring to the individual mandate, Medicaid expansion and insurance exchanges, the issues that have dominated the public debate so far. Buried in the enormous law are lesser-known provisions that are perhaps far more crucial to the long-term vitality of our health care system than merely expanding coverage.

Since 2010, the law has provided more than $1 billion for evidence-based medicine research, in which doctors and scientists collect and analyze patient data to determine whether treatments actually work. For example, UCSF is conducting a clinical trial of 100,000 women to determine if annual breast cancer screenings can better detect the disease than screenings that factor in a patient’s genetics and breast density.

But shouldn’t we already know which treatments work best, especially when we spend the most per capita on health care in the world? In the United States, doctors often prescribe medicines and procedures based on individual beliefs rather than any gold standard of treatment, because no such standards exist. The result is that patients with the same disease can receive wildly different treatments with wildly different outcomes.

For all of its flaws, the Affordable Care Act was the first serious attempt by the federal government to start to fix this defect. Since Medicare and Medicaid subsidize most health care in the country, the law signaled to the industry that taxpayer dollars are finite, that doctors, hospitals and companies that want to get paid must start to seriously think about which treatments offer the best results for patients.

If the feds don’t make this a priority, it’s hard to imagine that we can seriously reform health care.

Obamacare repeal ignores real problems with U.S. health care

Dr. Laura Esserman of UCSF has a grant to study results of breast cancer screenings and subsequent treatments.

Photo: Gabrielle Lurie, The Chronicle

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Dr. Laura Esserman (center) laughs during a phone call as she works with researchers Kenny Wimmer (left) and Roxanna Firouzian (right) in San Francisco, California, on Thursday, March 9, 2017.

Photo: Gabrielle Lurie, The Chronicle

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Dr. Laura Esserman (center) chats with researcher Kenny Wimmer (left) during a meeting in a conference room in San Francisco, California, on Thursday, March 9, 2017.

Photo: Gabrielle Lurie, The Chronicle

Repealing the law “will be a setback,” said Harry Nelson, a health care consultant and managing partner of Los Angeles law firm Nelson Hardiman. He is also the author of “From Obamacare to TrumpCare: Why You Should Care.” “Until now, the government has been leading the way.”

Congress has only recently begun to debate repealing and replacing the law, so anything can still happen. But both House Speaker Paul Ryan and Health and Human Services Secretary Tom Price have expressed opposition to the feds getting involved with the research.

“This is, obviously, still an evolving situation,” Christine Stencel, a spokeswoman for the federal Patient-Centered Outcomes Research Institute, wrote in an email. “Many more steps and actions are still to come.” Still unknown, she said, are Congress’ final actions, their timing or how they might affect the agency, which is in charge of administering the money that goes toward evidence-based research.

Despite the nation’s wealth (or perhaps because of it, as I will later explain), the U.S. health care system is a mess. In 2014, the country spent $9,403 per person on health care, by far the most of any nation, according to the World Bank. By contrast, Canada spent $5,292.

Yet Canadians seem to get more value. In 2015, the average life expectancy of a Canadian man was 80 years, according to the World Health Organization. For women, it was even better: 84 years.

In the United States, the comparable numbers were 77 for men and 82 for women.

“The U.S. health care system is the most expensive in the world, but gets really mediocre outcomes,” Nelson said.

There are two big reasons for this dysfunction. First, U.S. health care is based on a fee-for-service system; in other words, doctors get paid not for outcomes but for the services they perform. That kind of financial incentive can motivate doctors to offer patients more treatment, not better ones.

“If I get paid for doing stuff, then I’m going to do more stuff,” said Dr. Jeffrey Lobosky, an associate clinical professor at UCSF and director of neurosurgery at Enloe Medical Center’s intensive care unit in Chico. He was not referring to himself but rather how the system can produce such a mentality.

The second is a cultural reason. In the United States, we often tend to assume that things that are new, quicker or more expensive are superior to those older, slower or cheaper.

For example, a doctor offers a patient with a bad back two options: surgery to install a next-generation device developed by Medtronic, or taking ibuprofen and going to physical therapy twice a week. Without knowing which works best, many patients may opt for the more radical, costly option.

That’s why the Affordable Care Act established the Patient-Centered Outcomes Research Institute, which is funded by taxpayers and a fee on private insurance and self-insured health plans.

Since its inception, the group has spent more than $1 billion on studies that try to determine best practices for treating diseases, according to the institute’s most recent annual report. Researchers essentially analyze large pools of data to see if one treatment produces a better result than others.

In 2015, six researchers from UCSF received money to conduct such studies. Dr. Laura Esserman, a professor of surgery and director of the Carol Franc Buck Breast Care Center at UCSF, is one of the recipients.

The institute “set up an infrastructure to do vital research,” Esserman said. “It has put us in a position to really improve our services.”

Esserman is focusing on breast cancer screening. Until recently, doctors normally recommended that women start getting annual mammograms by age 40. But screenings can lead to inaccurate results that often do more damage than good, she said.

For example, a screening might detect a lump, but a follow-up biopsy, which can be invasive and painful, shows the lump is not cancerous. Or doctors might choose to aggressively treat a lump that might not have developed into full-blown cancer.

“Not everyone has the same risk,” Esserman said.

“People don’t understand that people are still going to get sick, whether they’re covered or not,” she said. “We’re going to spend the resources to treat them one way or the other, so we might as well spend the resources the right way.”

Top Republicans, however, are suspicious of federal management of health care programs. Price, who is a doctor himself, has argued that the government should not interfere with the relationship between doctor and patient. He also fears that the feds will use data from evidence-based studies to deny reimbursements for treatments that might work for some patients.

As a congressman, Price repeatedly introduced legislation to bar the federal government from making payment decisions based on comparative effectiveness research. His bill, the Empowering Patients First Act, also seeks to prevent the Patient-Centered Outcomes Research Institute from releasing any data “until after consultation with and approved by relevant physician specialty organizations.”

Dr. Robert Pearl, CEO of the Permanente Medical Group, agrees with Price that physicians, not the government, should lead the drive to adopt evidence-based medicine. But Pearl also acknowledges that doctors can be the obstacle to such reform.

Physicians often suffer from “availability bias,” in which they assume the treatment that immediately comes to mind is the best option, without doing further research, said Pearl, author of “Mistreated: Why We Think We’re Getting Good Healthcare — And Why We’re Usually Wrong.”

“That’s just how our brains are wired,” Pearl said. “We rely on anecdotal information from a single patient versus large groups of data.”

So far, the debate over replacing the Affordable Care Act has centered on health insurance. But any law that focuses solely on coverage ignores the underlying flaw in the U.S. health care system: that we pay too much for too little.

Thomas Lee is a business columnist for the San Francisco Chronicle. He is the author of “Rebuilding Empires,” (Palgrave Macmillan/St. Martin’s Press), a book about the future of big box retail in the digital age. Lee has previously written for the Star Tribune (Minneapolis), St. Louis Post-Dispatch, Seattle Times and China Daily USA. He also served as bureau chief for two Internet news startups: MedCityNews.com and Xconomy.com.